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Coexpression cluster:C2937: Difference between revisions

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|full_id=C2937_placenta_Smooth_Fibroblast_chorionic_Lens_Aortic_Chondrocyte
|full_id=C2937_placenta_Smooth_Fibroblast_chorionic_Lens_Aortic_Chondrocyte
|id=C2937
|id=C2937
|ontology_enrichment_celltype=CL:0000055!1.49e-33!180;CL:0000187!1.70e-27!54;CL:0000680!3.74e-27!57;CL:0000056!3.74e-27!57;CL:0000355!3.74e-27!57;CL:0000192!1.45e-24!42;CL:0000514!1.45e-24!42;CL:0000183!3.30e-24!59;CL:0000393!1.26e-23!60;CL:0000211!1.26e-23!60;CL:0000359!1.03e-21!32;CL:0000057!9.70e-17!75;CL:0002494!1.59e-11!16;CL:0000222!2.79e-09!119;CL:0002539!5.38e-09!10;CL:0000048!1.20e-07!430;CL:0002334!5.18e-07!12;CL:0000723!5.39e-07!436
|ontology_enrichment_celltype=CL:0000680!2.22e-16!58;CL:0000056!2.22e-16!58;CL:0000355!2.22e-16!58;CL:0000187!1.02e-15!55;CL:0000057!2.42e-14!76;CL:0000183!5.93e-14!59;CL:0000393!3.65e-13!61;CL:0000211!3.65e-13!61;CL:0000192!4.33e-11!43;CL:0000514!4.33e-11!43;CL:0000048!2.18e-09!427;CL:0000359!3.54e-09!32;CL:0000723!7.17e-09!433;CL:0002334!1.09e-08!12;CL:0000034!3.27e-08!441;CL:0000055!5.21e-08!106;CL:0002494!8.30e-08!16;CL:0002620!1.00e-07!23
|ontology_enrichment_disease=DOID:2394!6.00e-08!14
|ontology_enrichment_disease=DOID:2394!2.91e-10!14
|ontology_enrichment_uberon=UBERON:0001134!5.05e-25!61;UBERON:0002036!5.05e-25!61;UBERON:0003082!5.05e-25!61;UBERON:0004290!4.31e-24!70;UBERON:0000914!5.45e-24!83;UBERON:0002329!5.45e-24!83;UBERON:0003077!5.45e-24!83;UBERON:0003059!5.45e-24!83;UBERON:0007282!5.45e-24!83;UBERON:0009618!5.45e-24!83;UBERON:0007285!5.45e-24!83;UBERON:0002385!1.60e-23!63;UBERON:0001015!1.60e-23!63;UBERON:0000383!1.60e-23!63;UBERON:0000486!1.04e-20!82;UBERON:0004872!4.35e-18!84;UBERON:0001637!2.90e-16!42;UBERON:0003509!2.90e-16!42;UBERON:0004572!2.90e-16!42;UBERON:0004573!7.57e-15!33;UBERON:0004571!7.57e-15!33;UBERON:0004535!2.91e-13!110;UBERON:0000948!4.25e-13!24;UBERON:0005498!4.25e-13!24;UBERON:0004140!4.25e-13!24;UBERON:0009881!4.25e-13!24;UBERON:0004141!4.25e-13!24;UBERON:0003084!4.25e-13!24;UBERON:0007005!4.25e-13!24;UBERON:0004139!4.25e-13!24;UBERON:0004291!4.25e-13!24;UBERON:0001981!7.67e-13!60;UBERON:0007500!7.67e-13!60;UBERON:0004537!7.67e-13!60;UBERON:0006965!7.67e-13!60;UBERON:0002049!1.01e-12!79;UBERON:0007798!1.01e-12!79;UBERON:0005256!1.89e-12!143;UBERON:0001009!2.48e-12!113;UBERON:0007100!1.17e-10!27;UBERON:0002100!2.07e-10!216;UBERON:0003914!2.27e-10!118;UBERON:0000055!2.87e-09!69;UBERON:0004237!5.38e-09!10;UBERON:0004695!5.38e-09!10;UBERON:0002111!5.38e-09!10;UBERON:0004178!5.38e-09!10;UBERON:0000490!9.39e-09!138;UBERON:0000475!1.42e-08!365;UBERON:0000481!1.77e-08!347;UBERON:0001135!1.77e-08!15;UBERON:0003104!1.63e-07!238;UBERON:0009142!1.63e-07!238;UBERON:0004923!1.94e-07!57;UBERON:0000947!5.69e-07!21;UBERON:0010191!5.69e-07!21;UBERON:0000478!6.42e-07!24;UBERON:0000483!8.66e-07!309
|ontology_enrichment_uberon=UBERON:0001134!1.28e-14!62;UBERON:0002036!1.28e-14!62;UBERON:0003082!1.28e-14!62;UBERON:0002385!7.90e-14!64;UBERON:0001015!7.90e-14!64;UBERON:0000383!7.90e-14!64;UBERON:0007524!1.47e-13!73;UBERON:0002329!3.34e-13!71;UBERON:0003059!3.34e-13!71;UBERON:0007282!3.34e-13!71;UBERON:0004290!3.34e-13!71;UBERON:0009618!3.34e-13!71;UBERON:0003077!7.23e-13!72;UBERON:0007285!7.23e-13!72;UBERON:0000486!3.49e-12!83;UBERON:0007503!4.69e-11!78;UBERON:0004872!1.35e-09!83;UBERON:0004573!1.65e-09!33;UBERON:0004571!1.65e-09!33;UBERON:0004535!1.86e-08!109;UBERON:0001637!3.31e-08!42;UBERON:0003509!3.31e-08!42;UBERON:0004572!3.31e-08!42;UBERON:0001009!6.08e-08!112;UBERON:0001135!1.07e-07!15;UBERON:0002049!1.36e-07!78;UBERON:0007798!1.36e-07!78;UBERON:0000948!2.50e-07!24;UBERON:0005498!2.50e-07!24;UBERON:0004140!2.50e-07!24;UBERON:0009881!2.50e-07!24;UBERON:0004141!2.50e-07!24;UBERON:0003084!2.50e-07!24;UBERON:0007005!2.50e-07!24;UBERON:0004139!2.50e-07!24;UBERON:0004291!2.50e-07!24;UBERON:0000947!3.08e-07!21;UBERON:0010191!3.08e-07!21
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282,0.0347823,0.000978043,0.243319,0.0637178,0.036377,0.00559963,0.0147214,0.0280285,0.00273651,0.219023,0.115115,0.124916,0.0149794,0.0451304,0.0103095,6.02055e-06,0.00641248,0.224626,0.183585,0.271662,0.03989,0.171436,0.00177091,0.0691994,0.268299,0.198844,0.104946,0.127738,0.00176575,0.161213,0.00737926,2.62032e-10,0.0734014,0.0752771,0.178782,0.019419,0.00386504,0.271849,0.044355,0.105411,0.0997542,0.000105944,0.00315928,0.0725263,0.102587,0.00282365,0.00155767,0.0457886,0.0514927,0.324236,0.0262915,0.0367692,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0013909,0.00318372,0.515487,0.159873,0.000539412,0.0108948,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.0187556,0.32305,0.00454179,0.0328172,0.170848,0.487259,0.302909,0.363016,0.000181206,0.00222156,0.00601454,0.0303023,0.00237223,0.191914,0.184022,0.0253522,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.186295,0.173134,0.00537703,0.142875,0.167635,0.171311,0.0721023,0.00885745,9.98935e-07,0.00888201,0.002238,4.90356e-10,0.000176815,1.10883e-05,0.187329,0.0451012,0.000167509,0.0705088,0.107849,0.0560157,0.0430331,0.365775,0.155708,0.248017,0.000157747,0.652972,0.0760151,0.0629459,0.00483066,9.19079e-05,0.0278785,0.0832234,0.0939463,0.286748,0.0114526,0.0471607,0.163865,0.0278061,0.108863,0.307186,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0051212,0.0604041,0.144185,0.0925862,0.0466818,0.199201,0.049937,0.172796,0.00180935,0.071232,0.0117528,0.00776177,0.0269564,0.000482136,0.00484807,0.0754883,0.0501465,0.100006,0.0756617,0.0210009,0.0345492,0.279874,1.54864e-05,0.00022115,0.0271325,0.0189842,8.07734e-05,6.77006e-16,0.000213802,0.193021,0.240896,0.202165,0.00463136,0.00758581,0.079499,0.18762,7.86536e-05,0.127688,0.201169,0.220353,0.034089,0.00109671,0.291976,0.0578865,0.364334,0.15547,0.110256,0.101581,0.14794,0.147307,0.240761,0.225961,0.124417,0.0639386,0.317428,0.182843,0.130771,0.327768,0.00966571,0.147842,0.0339286,0.0255494,0.119015,0.00709584,0.21618,0.0323312,0.107021,0.0310605,9.16284e-05,0.0896967,0.0724243,8.40202e-05,0.315336,0.00246552,2.41864e-05,0.295555,0.154895,0.00214569,0.0478217,0.158752,0.0155059,0.0575231,0.174063,0.514243,0.1267,0.0466753,0.00568499,0.00555197,0.0895871,0.0434876,4.49595e-05,1.27355e-05,0.548059,0.25423,0.490559,3.81759e-05,0.153911,0.0272171,0.322168,0.0510811,0.174869,0.000399183,0.029441,0.0131065,0.23695,0.184287,0.0778742,0.14959,0.293249,1.70066e-06,0.622694,1.04077e-06,0.0284983,0.010661,0.241059,0.000126158,2.29142e-06,0.0768516,0.212703,0.56318,0.364079,0.107716,0.579886,2.32208e-05,0.569409,0.328518,1.89791e-05,6.52081e-09,0.0529131,0.142433,2.66735e-06,0.0201581,0.209437,0.000136886,0.0514874,0.598945,0.0016718,0.12974,0.0572812,0.214786,0.0181398,0.000629358,0.0500888,0.261575,0.257956,0.264245,0.379063,0.326516,0.000121546,0.436016,0.475063,0.202522,0.183837,0.158557,0.0083072,0.000177476,0.442469,0.212239,0.294954,0.156999,0.35974,0.0999766,0.39549,0.234254,0.357409,0.328421,0.0408829,0.50338,0.000504793,0.0158343,0.0563812,1.93444e-06,0.715362,0.139684,9.2614e-06,0.172925,0.00410246,0.044968,0.00629645,1.04293e-05,0.563206,0.00957951,0.321001,0.263302,0.00919591,0.0174164,0.189249,0.216102,0.254659,0.109605,0.000183912,0.0585759,7.52123e-06,0.000244281,0.0255104,0.0782409,0.156131,0.0237654,0.639483,0.0295677,0.452129,0.301581,0.261657,0.346776,0.466529,0.545655,0.114247,0.00100741,0.741477,0.385425,0.0531591,0.128211,0.386339,0.382854,0.00249494,0.139139,0.611661,5.14014e-05,0.136743,0.00154102,0.241014,0.282281,0.0159965,0.2536,0.246827,0.564333,0.00849832,8.73198e-07,0.050476,0.0738474,0.668972,0.000260496,6.21932e-07,0.0685505,0.0243196,0.348802,0.00438353,0.0574793,0.119749,0.00027375,0.254628,0.00910372,0.479347,1.10357e-07,0.632833,0.378333,0.00260167,0.264038,0.0282238,0.102495,0.350933,0.0383658,0.0446972,0.24452,0.0613938,0.0029143,0.0947248,1.3845e-08,0.210656,0.246234,0.211271,0.000381355,0.267248,0.118257,0.125087,0.0250035,0.321224,0.469461,0.325254,1.84818e-05,0.187728,0.231754,0.0340704,0.283107,0.00493982,0.427316,0.0890097,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.00686166,0.0450921,0.0887542,0.267811,0.338547,0.147872,0.0191872,0.293546,0.210125,0.292967,0.218414,0.00132289,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.0207461,0.201057,0.15696,0.129351,0.0105865,0.0786166,0.276997,0.205513,0.0442657,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.0429696,0.0138433,0.00272873,0.00277578,0.00468829,3.97258e-06,0.332769,0.262022,0.04166,0.000301342,0.184534,0.248707,0.31749,0.15156,0.287598,0.0554083,0.0271466,0.25788,0.181895,0.253768,0.30702,0.202977,4.4199e-05,0.0604859,0.0452813,0.222656,0.228479,1.27686e-05,0.037179,0.390754,0.355805,0.279739,0.00606762,0.0371525,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.00288876,0.298673,0.244395,0.0059278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}}
}}

Revision as of 14:35, 19 October 2012


Full id: C2937_placenta_Smooth_Fibroblast_chorionic_Lens_Aortic_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr9:118916164..118916178,+p5@PAPPA
Hg19::chr9:118916299..118916318,-p@chr9:118916299..118916318
-
Hg19::chr9:119164028..119164048,+p@chr9:119164028..119164048
+
Hg19::chr9:119164077..119164096,+p@chr9:119164077..119164096
+


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue1.28e-1462
striated muscle tissue1.28e-1462
myotome1.28e-1462
muscle tissue7.90e-1464
musculature7.90e-1464
musculature of body7.90e-1464
dense mesenchyme tissue1.47e-1373
somite3.34e-1371
presomitic mesoderm3.34e-1371
presumptive segmental plate3.34e-1371
dermomyotome3.34e-1371
trunk paraxial mesoderm3.34e-1371
paraxial mesoderm7.23e-1372
presumptive paraxial mesoderm7.23e-1372
multilaminar epithelium3.49e-1283
epithelial vesicle4.69e-1178
splanchnic layer of lateral plate mesoderm1.35e-0983
systemic artery1.65e-0933
systemic arterial system1.65e-0933
cardiovascular system1.86e-08109
artery3.31e-0842
arterial blood vessel3.31e-0842
arterial system3.31e-0842
circulatory system6.08e-08112
smooth muscle tissue1.07e-0715
vasculature1.36e-0778
vascular system1.36e-0778
heart2.50e-0724
primitive heart tube2.50e-0724
primary heart field2.50e-0724
anterior lateral plate mesoderm2.50e-0724
heart tube2.50e-0724
heart primordium2.50e-0724
cardiac mesoderm2.50e-0724
cardiogenic plate2.50e-0724
heart rudiment2.50e-0724
aorta3.08e-0721
aortic system3.08e-0721
Disease
Ontology termp-valuen
ovarian cancer2.91e-1014


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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